Tools design DNA-nanotube logic

By
Eric Smalley,
Technology Research NewsResearchers
have recently begun to use DNA to assemble carbon nanotubes into transistors,
the building blocks of computer circuits.

Biological DNA molecules, made from long strings of four types of
bases attached to a sugar-phosphate backbone, hold instructions for making
the proteins that enable life's processes. Artificial DNA molecules can
be caused to self-assemble into various patterns, and can also be coaxed
to attach to objects like carbon nanotubes. Given the right design, DNA
molecules can assemble objects.

Carbon nanotubes are rolled-up sheets of carbon atoms that have
useful electrical properties and can be 1,000 times smaller than an E. Coli
bacterium. A nanometer is one millionth of a millimeter.

Researchers from Duke University are aiming to make the process
of assembling molecular-scale components easier with a suite of computer-aided
design (CAD) tools for designing computer circuits made from carbon nanotubes
assembled by DNA.

Such self-assembled, molecular-scale circuitry could be used to
make cheaper, higher-performance computers than are possible using today's
silicon-based chipmaking technologies.

The researchers' tools make it possible to design computer circuits
that could be assembled automatically by DNA, said Chris Dwyer, an assistant
professor of electrical and computer engineering at Duke University. "Our
tools enable the design and evaluation of the circuitry... based on a DNA
self-assembly process and carbon nanotubes."

The tools are designed to build computer circuits at a density of
2,500 transistors per square micron, which is about 30 times more closely
packed than devices made using current chipmaking technologies, according
to Dwyer. A micron is one thousandth of a millimeter.

Transistors are arranged into logic gates, which in turn are combined
by the millions into the complicated circuits that process and store data.
Being able to assemble individual nanotube transistors is the prerequisite
for developing a nanotube-based chipmaking technology. The key is finding
ways to combine them into logic circuits.

The tools use a DNA scaffold recently created by another Duke University
research team as the foundation for nanotube circuits. The scaffold is a
self-assembled, grid-like fabric of DNA molecules. The grid's cavities measure
20 nanometers across.

The DNA scaffold technology is still being developed, said Dwyer.
The scaffolding and tools are being developed in parallel; once the DNA
scaffold technology is ready "we need the ability to reason about the performance
of these devices, and the computer architectures they can lead to, [in order]
to make high-level strategic decisions such as how to restructure the flow
of information and how to execute computations," he said.

The researchers' DNA-nanotube circuit architecture uses pairs of
complementary sequences of DNA to connect the ends of the carbon nanotubes
to points on the DNA scaffold. Connecting a semiconducting nanotube across
the middle of a cavity and a metallic nanotube across the cavity perpendicular
to the first nanotube makes a field-effect nanotube transistor. The gate
electrodes in field-effect transistors produce an electric field that changes
the conductivity of the device's semiconductor channel.

The architecture also calls for attaching metallic nanowires along
the DNA segments that make up the scaffold on both the top and bottom sides.
To fill the gaps between the nanotubes at the intersections of the grid
and the points where the transistor nanotubes connect to the grid, the architecture
includes DNA sequences that attract metallic nanoparticles. Later in the
process, the nanoparticles attract metal atoms to form a chemically-assembled
solder.

Like traditional computer-aided design tools, the researchers' tools
allow users to design individual devices like logic gates, connect the devices
to form whole systems, generate a circuit layout, and produce a sequence
of assembly steps. The assembly plan includes specific DNA sequences as
well as the nanotube or nanoparticle component for each step.

The tools use specialized models that roughly gauge the performance
of circuits based on the low-level behavior of nanotube transistors, said
Dwyer. "With this evaluation we can estimate the speed and energy consumption
of our designs; we use this to inform our decision-making process and high-level
architectural simulators," he said.

In providing a framework for evaluating potential systems, they
are similar to the first generation of design tools geared toward microelectronics
that eventually lead to very large-scale integration (VLSI) computer-aided
design tools, he said.

Nanoelectronics, and particularly the self-assembly process, require
different ways of thinking about circuitry and how computations occur to
make the best of the technology, said Dwyer. "Our tools provide a foundation
for those future designs," he said. "Further down the road, we hope these
tools will mature to the level that present-day very large-scale integration
computer-aided design tools have -- this will make wider access to the new
technology possible."

The researchers' next step is to use the tools in simple designs,
said Dwyer. "We are currently assembling a simple DNA lattice that will
eventually be suitable for a NAND gate," he said.

A NAND, or Not AND, gate is one of the basic building blocks of
computer circuits. It contains two input signals and one output signal.
If either of the input signals is a 1, the output is 0.

One challenge is that the larger the DNA scaffold, the greater the
number of unique DNA sequences required to create circuits. The researchers
are working on minimizing the overall number of required sequences, according
to Dwyer.

The researchers' nanotech fabrication computer-aided design tools
could be used to carry out nanotube construction in five to ten years, said
Dwyer. Dwyer's research colleagues were Vijeta Johri, Moky Cheung, Jaidev
Patwardhan, Alvin Lebeck and Daniel Sorin. The work is slated to appear
in the September issue of Nanotechnology. The research was funded
by the National Science Foundation (NSF) and Duke University.